Manufacturing Deficiencies: Common FDA Quality Issues in Pharmaceuticals and Medical Devices

When you take a pill or use a medical device, you expect it to be safe, clean, and effective. But behind every medicine or device is a manufacturing process-and if that process fails, lives can be at risk. The U.S. Food and Drug Administration (FDA) doesn’t wait for problems to happen. They inspect facilities around the world, and in 2025, they’re finding the same mistakes over and over again. These aren’t minor slip-ups. They’re systemic failures that can lead to contaminated drugs, inaccurate dosages, or devices that don’t work when you need them most.

Aseptic Processing Failures Are the Top Issue

The most common problem the FDA finds? Aseptic processing failures. This means the environment where sterile products like injectables, eye drops, or IV solutions are made isn’t truly sterile. In 2025, nearly half (47%) of all warning letters cited this issue. It’s not just about cleaning surfaces. It’s about controlling air flow, protecting workers from shedding skin cells, and proving that your process works every single time.

One company, Health and Natural Beauty USA Corp., got a warning letter in July 2025 because their media fill studies-tests that simulate the filling process to check for contamination-were incomplete. Another, Creative Essences, Inc., was cited in September 2025 for letting employees work in sterile areas without proper gowning or training. These aren’t rare mistakes. They’re preventable. But when a facility skips these steps, it’s like leaving your front door unlocked in a high-crime neighborhood. The FDA doesn’t just notice. They act.

Data Integrity Problems Are Everywhere

Another major red flag: data integrity. In 39% of 2025 warning letters, the FDA found records that were falsified, missing, or manipulated. This isn’t about handwriting. It’s about electronic systems that don’t track who changed what, when, or why.

Guangxi Yulin Pharmaceutical Group Co. Ltd. got flagged because their UV-Vis and IR instruments didn’t have audit trails. That means no one could tell if someone deleted a failed test result or changed a number to make a batch look合格. Another company used laminated paper records with erasable markers-so someone could literally wipe out a bad result and rewrite it. The FDA calls this a violation of ALCOA+: records must be Attributable, Legible, Contemporaneous, Original, and Accurate-and plus, they must be complete.

These aren’t just paperwork problems. They’re trust problems. If you can’t trust the data, you can’t trust the product. And if you can’t trust the product, patients are at risk.

Materials Aren’t Being Tested Properly

What goes into a drug matters as much as how it’s made. In 35% of warning letters, the FDA found that raw materials weren’t properly tested. One shocking example: glycerin and sorbitol-common ingredients in cough syrups and toothpaste-weren’t checked for diethylene glycol (DEG), a toxic chemical linked to kidney failure and death.

Back in 2007-2009, DEG contamination in cough syrup killed over 100 people worldwide. The FDA has been watching for this ever since. Yet in 2025, Health and Natural Beauty USA Corp. still didn’t test for it. Other companies failed to verify that their suppliers were doing their own testing correctly. The FDA expects manufacturers to treat every ingredient like a potential threat. That means testing, validating, and documenting-not just trusting a label.

Processes Aren’t Validated

Just because a process worked once doesn’t mean it’ll work every time. Process validation is the science of proving your method consistently produces a safe, effective product. In 28% of 2025 warning letters, companies didn’t do this at all.

One company making toothpaste never validated their mixing or filling process. Another didn’t have scientifically sound methods to test their drug’s strength or purity. The FDA doesn’t accept “we’ve always done it this way.” They require proof: three consecutive batches made under controlled conditions, with every step monitored and recorded. If you can’t show that, your product isn’t approved.

Quality Culture Is the Real Problem

Here’s the hard truth: most of these issues aren’t accidental. They’re cultural. Dr. David Lim from Compliance Architects says 78% of the companies cited in 2025 warning letters had a leadership mindset that prioritized speed over safety. Production targets were met by cutting corners. Employees were afraid to speak up. Quality teams had no real authority.

One company in China didn’t even prepare batch production records for every batch. That’s not a mistake. That’s negligence. In India, 4 warning letters in 2025 pointed to data integrity failures tied to a lack of training and oversight. In Malaysia, the quality unit was weak-often staffed by people with no real power to stop production.

The FDA isn’t just looking for technical violations anymore. They’re looking at who’s in charge, how decisions are made, and whether quality is treated as a core value-or an afterthought. That’s why they launched the Quality Management Maturity (QMM) program in 2024. It’s voluntary, but by late 2025, 87 companies were already participating. And here’s the kicker: those companies saw 63% fewer repeat violations and fixed problems 41% faster.

What Happens When You Get Caught?

If the FDA finds serious issues, they don’t just send a letter. They block your products. As of November 20, 2025, 147 facilities are on Import Alert 66-40. That means every shipment from those sites gets stopped at the U.S. border. No exceptions. No paperwork fixes. You need a full, independent audit and a plan approved by the FDA before your products can even be considered for entry.

Remediation isn’t quick. It takes 6 to 18 months. You’ll need to hire an independent CGMP consultant (required in 92% of 2025 warning letters). You’ll need to rebuild your data systems with validated audit trails that retain records for at least 180 days. You’ll need to retrain everyone-from the lab tech to the CEO.

And it’s getting harder. The FDA increased unannounced foreign inspections by 40% in 2025. They’re now targeting domestic sites too, planning 1,200 unannounced inspections in 2026-up from 850 in 2025. This isn’t a crackdown. It’s a new normal.

Where Are the Biggest Risks?

China, India, and Malaysia account for 73% of all 2025 warning letters. But the problems aren’t random:

• China: 28 warning letters cited failures in analytical method validation-meaning they couldn’t prove their tests actually measured what they claimed.
• India: 24 letters focused on data integrity, often due to poor training and lack of oversight.
• Malaysia: 9 letters pointed to weak quality units with no authority to halt production.

These aren’t regional stereotypes. They’re patterns the FDA has tracked for years. And they’re not going away unless companies invest in real change, not just paperwork.

What’s Next for Manufacturers?

The FDA’s focus is shifting. In November 2025, Commissioner Robert Califf said QMM assessment results might start influencing how often a facility gets inspected. That means companies with strong quality cultures could see fewer inspections. Those with weak ones? More scrutiny.

Emerging issues are also on the radar:

• Digital quality systems: 12 warning letters in 2025 cited poor controls for cloud-based software.
• Supply chain transparency: 8 letters targeted companies that didn’t properly monitor contract labs.
• Advanced manufacturing: 5 letters flagged issues with continuous manufacturing-new tech that’s great, but only if you validate it right.

The message is clear: quality isn’t a department. It’s a system. And if you’re treating it like a checkbox, you’re already behind.

What Should You Do If You’re a Manufacturer?

If you’re making drugs or devices for the U.S. market, here’s what you need to do now:

1. Review your aseptic controls. Are your media fills up to date? Is your gowning protocol enforced? Can you prove sterility?
2. Fix your data systems. No more erasable pens. No more untracked electronic records. Audit trails must be enabled, secure, and retained for 180+ days.
3. Test your inputs. Don’t assume your supplier’s certificate is enough. Validate your own testing, especially for high-risk materials like glycerin.
4. Validate your processes. Three batches. Full documentation. Acceptance criteria defined before you start.
5. Fix your culture. Does your CEO care more about deadlines or safety? If the answer isn’t safety, you’re one inspection away from disaster.

The FDA isn’t trying to shut you down. They’re trying to protect patients. And if your quality system can’t do that, they’ll find out-and they’ll stop you.